Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations.

Biomolecular condensates are phase separated systems that play an important role in the spatio-temporal organisation of cells. Their distinct physico-chemical nature offers a unique environment for chemical reactions to occur. The compartmentalisation of chemical reactions is also believed to be central to the development of early life. To demonstrate how molecular dynamics may be used to capture chemical reactions in condensates, here we perform reactive molecular dynamics simulations using the coarse-grained Martini forcefield. We focus on the formation of rings of benzene-1,3-dithiol inside a synthetic peptide-based condensate, and find that the ring size distribution shifts to larger macrocycles compared to when the reaction takes place in an aqueous environment. Moreover, reaction rates are noticeably increased when the peptides simultaneously undergo phase separation, hinting that condensates may act as chaperones in recruiting molecules to reaction hubs.

Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond.

Water is often the testing ground for new, advanced force fields. While advanced functional forms for intermolecular interactions have been integral to the development of accurate water models, less attention has been paid to a transferable model for intramolecular valence terms. In this work, we present a one-body energy and dipole moment surface model, named 1B-UCB, that is simple yet accurate and can be feasibly adapted for both standard and advanced potentials. 1B-UCB for water is comparable in accuracy to those with much more complex functional forms, despite having drastically fewer parameters. The parametrization protocol has been implemented as part of the Q-Force automated workflow and requires only a quantum mechanical Hessian calculation as reference data, hence allowing it to be easily extended to a variety of molecular systems beyond water, which we demonstrate on a selection of small molecules with different symmetries.

M-Chem: a Modular Software Package for Molecular Simulation that Spans Scientific Domains.

We present a new software package called M-Chem that is designed from scratch in C++ and parallelized on shared-memory multi-core architectures to facilitate efficient molecular simulations. Currently, M-Chem is a fast molecular dynamics (MD) engine that supports the evaluation of energies and forces from two-body to many-body all-atom potentials, reactive force fields, coarse-grained models, combined quantum mechanics molecular mechanics (QM/MM) models, and external force drivers from machine learning, augmented by algorithms that are focused on gains in computational simulation times. M-Chem also includes a range of standard simulation capabilities including thermostats, barostats, multi-timestepping, and periodic cells, as well as newer methods such as fast extended Lagrangians and high quality electrostatic potential generation. At present M-Chem is a developer friendly environment in which we encourage new software contributors from diverse fields to build their algorithms, models, and methods in our modular framework. The long-term objective of M-Chem is to create an interdisciplinary platform for computational methods with applications ranging from biomolecular simulations, reactive chemistry, to materials research.

Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations.

Chemical reactions are ubiquitous in both materials and the biophysical sciences. While coarse-grained (CG) molecular dynamics simulations are often needed to study the spatiotemporal scales present in these fields, chemical reactivity has not been explored thoroughly in CG models. In this work, a new approach to model chemical reactivity is presented for the widely used Martini CG Martini model. Employing tabulated potentials with a single extra particle for the angle dependence, the model provides a generic framework for capturing bonded topology changes using nonbonded interactions. As a first example application, the reactive model is used to study the macrocycle formation of benzene-1,3-dithiol molecules through the formation of disulfide bonds. We show that starting from monomers, macrocycles with sizes in agreement with experimental results are obtained using reactive Martini. Overall, our reactive Martini framework is general and can be easily extended to other systems. All of the required scripts and tutorials to explain its use are provided online.

Strategies for Enhancing the Dielectric Constant of Organic Materials.

High dielectric constant organic semiconductors, often obtained by the use of ethylene glycol (EG) side chains, have gained attention in recent years in the efforts of improving the device performance for various applications. Dielectric constant enhancements due to EGs have been demonstrated extensively, but various effects, such as the choice of the particular molecule and the frequency and temperature regime, that determine the extent of this enhancement require further understanding. In this work, we study these effects by means of polarizable molecular dynamics simulations on a carefully selected set of fullerene derivatives with EG side chains. The selection allows studying the dielectric response in terms of both the number and length of EG chains and also the choice of the group connecting the fullerene to the EG chain. The computed time- and frequency-dependent dielectric responses reveal that the experimentally observed rise of the dielectric constant within the kilo/megahertz regime for some molecules is likely due to the highly stretched dielectric response of the EGs: the initial sharp increase over the first few nanoseconds is followed by a smaller but persistent increase in the range of microseconds. Additionally, our computational protocol allows the separation of different factors that contribute to the overall dielectric constant, providing insights to make several molecular design guides for future organic materials in order to enhance their dielectric constant further.

Modelling structural properties of cyanine dye nanotubes at coarse-grained level.

Self-assembly is a ubiquitous process spanning from biomolecular aggregates to nanomaterials. Even though the resulting aggregates can be studied through experimental techniques, the dynamic pathways of the process and the molecular details of the final structures are not necessarily easy to resolve. Consequently, rational design of self-assembling aggregates and their properties remains extremely challenging. At the same time, modelling the self-assembly with computational methods is not trivial, because its spatio-temporal scales are usually beyond the limits of all-atom based simulations. The use of coarse-grained (CG) models can alleviate this limitation, but usually suffers from the lack of optimised parameters for the molecular constituents. In this work, we describe the procedure of parametrizing a CG Martini model for a cyanine dye (C8S3) that self-assembles into hollow double-walled nanotubes. First, we optimised the model based on quantum mechanics calculations and all-atom reference simulations, in combination with available experimental data. Then, we conducted random self-assembly simulations, and the performance of our model was tested on preformed assemblies. Our simulations provide information on the time-dependent local arrangement of this cyanine dye, when aggregates are being formed. Furthermore, we provide guidelines for designing and optimising parameters for similar self-assembling nanomaterials.

Fullerene derivatives with oligoethylene-glycol side chains: an investigation on the origin of their outstanding transport properties.

For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V-1 s-1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications.

Q-Force: Quantum Mechanically Augmented Molecular Force Fields.

The quality of molecular dynamics simulations strongly depends on the accuracy of the underlying force fields (FFs) that determine all intra- and intermolecular interactions of the system. Commonly, transferable FF parameters are determined based on a representative set of small molecules. However, such an approach sacrifices accuracy in favor of generality. In this work, an open-source and automated toolkit named Q-Force is presented, which augments these transferable FFs with molecule-specific bonded parameters and atomic charges that are derived from quantum mechanical (QM) calculations. The molecular fragmentation procedure allows treatment of large molecules (>200 atoms) with a low computational cost. The generated Q-Force FFs can be used at the same computational cost as transferable FFs, but with improved accuracy: We demonstrate this for the vibrational properties on a set of small molecules and for the potential energy surface on a complex molecule (186 atoms) with photovoltaic applications. Overall, the accuracy, user-friendliness, and minimal computational overhead of the Q-Force protocol make it widely applicable for atomistic molecular dynamics simulations.

Amphipathic Side Chain of a Conjugated Polymer Optimizes Dopant Location toward Efficient N-Type Organic Thermoelectrics.

There is no molecular strategy for selectively increasing the Seebeck coefficient without reducing the electrical conductivity for organic thermoelectrics. Here, it is reported that the use of amphipathic side chains in an n-type donor-acceptor copolymer can selectively increase the Seebeck coefficient and thus increase the power factor by a factor of ≈5. The amphipathic side chain contains an alkyl chain segment as a spacer between the polymer backbone and an ethylene glycol type chain segment. The use of this alkyl spacer does not only reduce the energetic disorder in the conjugated polymer film but can also properly control the dopant sites away from the backbone, which minimizes the adverse influence of counterions. As confirmed by kinetic Monte Carlo simulations with the host-dopant distance as the only variable, a reduced Coulombic interaction resulting from a larger host-dopant distance contributes to a higher Seebeck coefficient for a given electrical conductivity. Finally, an optimized power factor of 18 µW m-1 K-2 is achieved in the doped polymer film. This work provides a facile molecular strategy for selectively improving the Seebeck coefficient and opens up a new route for optimizing the dopant location toward realizing better n-type polymeric thermoelectrics.

N-type organic thermoelectrics: demonstration of ZT > 0.3.

The 'phonon-glass electron-crystal' concept has triggered most of the progress that has been achieved in inorganic thermoelectrics in the past two decades. Organic thermoelectric materials, unlike their inorganic counterparts, exhibit molecular diversity, flexible mechanical properties and easy fabrication, and are mostly 'phonon glasses'. However, the thermoelectric performances of these organic materials are largely limited by low molecular order and they are therefore far from being 'electron crystals'. Here, we report a molecularly n-doped fullerene derivative with meticulous design of the side chain that approaches an organic 'PGEC' thermoelectric material. This thermoelectric material exhibits an excellent electrical conductivity of >10 S cm-1 and an ultralow thermal conductivity of <0.1 Wm-1K-1, leading to the best figure of merit ZT = 0.34 (at 120 °C) among all reported single-host n-type organic thermoelectric materials. The key factor to achieving the record performance is to use 'arm-shaped' double-triethylene-glycol-type side chains, which not only offer excellent doping efficiency (~60%) but also induce a disorder-to-order transition upon thermal annealing. This study illustrates the vast potential of organic semiconductors as thermoelectric materials.

How Ethylene Glycol Chains Enhance the Dielectric Constant of Organic Semiconductors: Molecular Origin and Frequency Dependence.

Incorporating ethylene glycols (EGs) into organic semiconductors has become the prominent strategy to increase their dielectric constant. However, EG's contribution to the dielectric constant is due to nuclear relaxations, and therefore, its relevance for various organic electronic applications depends on the time scale of these relaxations, which remains unknown. In this work, by means of a new computational protocol based on polarizable molecular dynamics simulations, the time- and frequency-dependent dielectric constant of a representative fullerene derivative with EG side chains is predicted, the origin of its unusually high dielectric constant is explained, and design suggestions are made to further increase it. Finally, a dielectric relaxation time of ∼1 ns is extracted which suggests that EGs may be too slow to reduce the Coulombic screening in organic photovoltaics but are definitely fast enough for organic thermoelectrics with much lower charge carrier velocities.

Can the Dielectric Constant of Fullerene Derivatives Be Enhanced by Side-Chain Manipulation? A Predictive First-Principles Computational Study.

The low efficiency of organic photovoltaic (OPV) devices has often been attributed to the strong Coulombic interactions between the electron and hole, impeding the charge separation process. Recently, it has been argued that by increasing the dielectric constant of materials used in OPVs, this strong interaction could be screened. In this work, we report the application of periodic density functional theory together with the coupled perturbed Kohn-Sham method to calculate the electronic contribution to the dielectric constant for fullerene C60 derivatives, a ubiquitous class of molecules in the field of OPVs. The results show good agreement with experimental data when available and also reveal an important undesirable outcome when manipulating the side chain to maximize the static dielectric constant: in all cases, the electronic contribution to the dielectric constant decreases as the side chain increases in size. This information should encourage both theoreticians and experimentalists to further investigate the relevance of contributions to the dielectric constant from slower processes like vibrations and dipolar reorientations for facilitating the charge separation, because electronically, enlarging the side chain of conventional fullerene derivatives only lowers the dielectric constant, and consequently, their electronic dielectric constant is upper bound by the one of C60.

Biobased Chemicals: 1,2,4-Benzenetriol, Selective Deuteration and Dimerization to Bifunctional Aromatic Compounds.

1,2,4-Benzenetriol (BTO), sourced from the carbohydrate-derived platform chemical 5-hydroxylmethylfurfural (HMF), is an interesting starting point for the synthesis of various biobased aromatic products. However, BTO readily undergoes dimerization and other reactions under mild conditions, making analysis and isolation challenging. To both control and utilize the reactivity of BTO to produce biobased building blocks, its reactivity needs to be better understood. Here it was found that specific BTO aromatic C-H bonds are reactive toward deuterium exchange with D2O, which appears pronounced under acidic conditions at room temperature and can lead to the selective formation of BTO with an aromatic ring that contains one or two deuterium atoms, the first at the five and the second at the three position. By exposure to air, it was shown that BTO forms a 5,5'-linked BTO dimer [1,1'-biphenyl]-2,2',4,4',5,5'-hexaol (1) and subsequently a hydroxyquinone containing dimeric structure 2',4,4',5'-tetrahydroxy-[1,1'-biphenyl]-2,5-dione (2). Additionally, condensed dimer dibenzo[b,d]furan-2,3,7,8-tetraol (3) can be relatively easily accessed. The controlled formation of these symmetric and asymmetric multifunctional dimers illustrates diverse possibilities for BTO to be converted to valuable biobased aromatic compounds. Deuterium exchange was attributed to electrophilic aromatic substitution because this reactivity was found to be independent of oxygen and acid mediated. On the contrary, the dimerization was dependent on the presence of oxygen and thus likely involves radical intermediates. Thus this report overall displays different accessible reaction pathways for BTO that can be exploited for the production of BTO-derived compounds.